Variant report

Variant	rs6712517
Chromosome Location	chr2:98340364-98340365
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98340167..98342272-chr2:98350738..98353485,2	MCF-7	breast:
2	chr2:98331870..98333821-chr2:98339114..98340858,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115085	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10182941	0.84[CEU][hapmap]
rs11123869	0.82[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs12712174	0.84[CEU][hapmap]
rs1317178	0.84[CEU][hapmap]
rs1466020	1.00[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1922282	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs2309316	0.84[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap]
rs4274643	0.84[CEU][hapmap]
rs6543108	0.84[CEU][hapmap]
rs6709571	0.84[CEU][hapmap]
rs7558931	0.84[CEU][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap]
rs7567397	0.84[CEU][hapmap]
rs873886	1.00[LWK][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv874696	chr2:98309882-98362907	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv33510	chr2:98317103-98341302	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3370785	chr2:98339370-98341868	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv10104	chr2:98340272-98345152	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6712517	CNNM3	cis	cerebellum	SCAN
rs6712517	TMEM131	Cis_1M	lymphoblastoid	RTeQTL
rs6712517	ADRA2B	cis	cerebellum	SCAN
rs6712517	FAM178B	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98333600-98341800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:98335000-98344800	Weak transcription	Right Atrium	heart
3	chr2:98336000-98340400	Weak transcription	Spleen	Spleen
4	chr2:98336000-98344400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr2:98336000-98346000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
6	chr2:98336200-98345000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr2:98336200-98345600	Genic enhancers	Primary T cells fromperipheralblood	blood
8	chr2:98336200-98345800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr2:98336200-98351200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:98336400-98345000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:98336400-98346000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
12	chr2:98336400-98361400	Weak transcription	Primary B cells from cord blood	blood
13	chr2:98336600-98346200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr2:98336600-98346200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:98336600-98358800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:98337400-98343800	Strong transcription	Fetal Thymus	thymus
17	chr2:98337400-98346600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:98337800-98343200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:98337800-98357400	Strong transcription	Dnd41	blood
20	chr2:98338600-98340400	Enhancers	Placenta	Placenta
21	chr2:98338600-98341000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr2:98338800-98358800	Strong transcription	Thymus	Thymus
23	chr2:98339200-98341400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:98339200-98345800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr2:98339400-98342800	Weak transcription	HSMMtube	muscle
26	chr2:98339600-98340800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:98339600-98357200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:98339800-98341800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr2:98339800-98341800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr2:98339800-98342000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr2:98339800-98342200	Strong transcription	Primary T cells from cord blood	blood
32	chr2:98340000-98340600	ZNF genes & repeats	Esophagus	oesophagus
33	chr2:98340000-98341600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:98340200-98341000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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